This study compares the microbial load associated with smoked fish (Chrysichthys nigrodigitatus) from Oyan lake and Ogun waterside in Ogun State. Three samples each were purchased from Lafenwa and Makun-omi markets respectively. Microbial load in the skin, intestine and gills were assessed using Macconky Agar (MA), and Nutrient Agar (NA) to isolate bacteria while Sabouraud Dextrose Agar (SDA) was used to isolate fungi. The average bacterial counts for all the samples ranged from 3.1 x106 to 4.9 x106 in makun market while 6.8 x106 to 13.8 x106 in lafenwa market has the highest bacteria count. The microorganism isolated and identified in the markets include the following families of bacteria: Bacillus spp (10%, 10%), Micrococcus spp (10%, 10%), Staphylococcus saprophyticus (5%, 10%), Escherichia coli (10%, 15%) and Staphylococcus aureus (5%, 10%) of which Staphylococcus saprophyticus, Escherichia coli and Staphylococcus aureus percentage occurrence rate were higher in lafenwa market. The fungal family include; Fusarium spp (14.3%, 28.6%), Mucor spp (14.3%, 28.6%) and Aspergillus fumigatus (0.0%, 14.3%). The results therefore showed that smoked fish from Oyan lake were heavily contaminated than that of Ogun waterside when compared with the maximum recommended bacteria count for good quality product and this has effect on human health after consumption. The contamination of the surrounding environment with industrial and domestic waste should be controlled as well as ensure proper handling of fish. The health implication to consumers and the public health importance was also revealed in the stud